As a sophomore in 2008 he earned MVP honors at the National Amateur Baseball Championship, racking up 3 wins with a 0.00 ERA in 5 games.
In April 2009, Yoon won another MVP at the Spring Collegiate National Baseball Championship, posting 4-0 with a 0.27 ERA and 46 strikeouts in 33 innings.
Yoon finished the 2009 collegiate season with a record of 7-1 and an ERA of 0.15 in 61.1 innings pitched, and was named the best Korean amateur pitcher of the year.
In the series, he posted the lowest ERA (1.80) amongst the eight pitchers on the Korean roster, striking out 14 batters in 10 innings pitched.
In the bottom of the ninth inning of the second round game against Panama, Yoon entered with a 5-4 lead, two out and runners at first and third, and racked up a save, inducing a flyout to center from César Quintero.